+ PDBEntry pdbEntry = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB,
+ "x/y/z/File");
+
+ // id comparison is not case sensitive
+ PDBEntry case1 = new PDBEntry("1XYZ", "A", PDBEntry.Type.PDB,
+ "x/y/z/File");
+ // chain code comparison is not case sensitive
+ PDBEntry case2 = new PDBEntry("1xyz", "a", PDBEntry.Type.PDB,
+ "x/y/z/File");
+ // different type
+ PDBEntry case3 = new PDBEntry("1xyz", "A", PDBEntry.Type.FILE,
+ "x/y/z/File");
+ // different everything
+ PDBEntry case4 = new PDBEntry(null, null, null, null);
+ // null id
+ PDBEntry case5 = new PDBEntry(null, "A", PDBEntry.Type.PDB,
+ "x/y/z/File");
+ // null chain
+ PDBEntry case6 = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
+ "x/y/z/File");
+ // null type
+ PDBEntry case7 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
+ // null file
+ PDBEntry case8 = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB, null);
+ // identical to case7
+ PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
+ // different file only
+ PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
+
+ /*
+ * assertEquals will invoke PDBEntry.equals()
+ */
+ assertFalse(pdbEntry.equals(null));
+ assertFalse(pdbEntry.equals("a"));
+ assertEquals(case1, pdbEntry);
+ assertEquals(case2, pdbEntry);
+ assertNotEquals(case3, pdbEntry);
+ assertNotEquals(case4, pdbEntry);
+ assertNotEquals(case5, pdbEntry);
+ assertNotEquals(case6, pdbEntry);
+ assertNotEquals(case7, pdbEntry);
+ assertNotEquals(case8, pdbEntry);
+ assertEquals(case7, case9);
+ assertNotEquals(case9, case10);
+
+ // add properties
+ case7.setProperty("hello", "world");
+ assertNotEquals(case7, case9);
+ case9.setProperty("hello", "world");
+ assertEquals(case7, case9);
+ case9.setProperty("hello", "WORLD");
+ assertNotEquals(case7, case9);
+
+ /*
+ * change string wrapper property to string...
+ */
+ case1.setProperty("chain_code", "a");
+ assertFalse(pdbEntry.equals(case1));
+ assertFalse(case1.equals(pdbEntry));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetChainCode()
+ {
+ PDBEntry pdbEntry = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
+ "x/y/z/File");
+ assertNull(pdbEntry.getChainCode());
+
+ pdbEntry.setChainCode("a");
+ assertEquals("a", pdbEntry.getChainCode());
+
+ pdbEntry.setChainCode(null);
+ assertNull(pdbEntry.getChainCode());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetType()
+ {
+ assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("FILE"));
+ assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("File"));
+ assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file"));
+ assertNotSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file "));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testTypeMatches()
+ {
+ // TODO Type.matches() is not used - delete?
+ assertTrue(PDBEntry.Type.FILE.matches("FILE"));
+ assertTrue(PDBEntry.Type.FILE.matches("File"));
+ assertTrue(PDBEntry.Type.FILE.matches("file"));
+ assertFalse(PDBEntry.Type.FILE.matches("FILE "));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testUpdateFrom()
+ {
+ PDBEntry pdb1 = new PDBEntry("3A6S", null, null, null);
+ PDBEntry pdb2 = new PDBEntry("3A6S", null, null, null);
+ assertTrue(pdb1.updateFrom(pdb2));
+
+ /*
+ * mismatch of pdb id not allowed
+ */
+ pdb2 = new PDBEntry("1A70", "A", null, null);
+ assertFalse(pdb1.updateFrom(pdb2));
+ assertNull(pdb1.getChainCode());
+
+ /*
+ * match of pdb id is not case sensitive
+ */
+ pdb2 = new PDBEntry("3a6s", "A", null, null);
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getChainCode(), "A");
+ assertEquals(pdb1.getId(), "3A6S");
+
+ /*
+ * add chain - with differing case for id
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, null);
+ pdb2 = new PDBEntry("3a6s", "A", null, null);
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getChainCode(), "A");
+
+ /*
+ * change of chain is not allowed
+ */
+ pdb2 = new PDBEntry("3A6S", "B", null, null);
+ assertFalse(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getChainCode(), "A");
+
+ /*
+ * change chain from null
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, null);
+ pdb2 = new PDBEntry("3A6S", "B", null, null);
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getChainCode(), "B");
+
+ /*
+ * set file and type
+ */
+ pdb2 = new PDBEntry("3A6S", "B", Type.FILE, "filePath");
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getFile(), "filePath");
+ assertEquals(pdb1.getType(), Type.FILE.toString());
+ assertEquals(pdb1.getChainCode(), "B");
+ /*
+ * change of file is not allowed
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, "file1");
+ pdb2 = new PDBEntry("3A6S", "A", null, "file2");
+ assertFalse(pdb1.updateFrom(pdb2));
+ assertNull(pdb1.getChainCode());
+ assertEquals(pdb1.getFile(), "file1");
+
+ /*
+ * set type without change of file
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, "file1");
+ pdb2 = new PDBEntry("3A6S", null, Type.PDB, "file1");
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getType(), Type.PDB.toString());
+
+ /*
+ * set file with differing case of id and chain code
+ */
+ pdb1 = new PDBEntry("3A6S", "A", null, null);
+ pdb2 = new PDBEntry("3a6s", "a", Type.PDB, "file1");
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getType(), Type.PDB.toString());
+ assertEquals(pdb1.getId(), "3A6S"); // unchanged
+ assertEquals(pdb1.getFile(), "file1"); // updated
+ assertEquals(pdb1.getChainCode(), "A"); // unchanged
+
+ /*
+ * changing nothing returns true
+ */
+ pdb1 = new PDBEntry("3A6S", "A", Type.PDB, "file1");
+ pdb2 = new PDBEntry("3A6S", null, null, null);
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getChainCode(), "A");
+ assertEquals(pdb1.getType(), Type.PDB.toString());
+ assertEquals(pdb1.getFile(), "file1");
+
+ /*
+ * add and update properties only
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, null);
+ pdb2 = new PDBEntry("3A6S", null, null, null);
+ pdb1.setProperty("destination", "mars");
+ pdb1.setProperty("hello", "world");
+ pdb2.setProperty("hello", "moon");
+ pdb2.setProperty("goodbye", "world");
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getProperty("destination"), "mars");
+ assertEquals(pdb1.getProperty("hello"), "moon");
+ assertEquals(pdb1.getProperty("goodbye"), "world");
+
+ /*
+ * add properties only
+ */
+ pdb1 = new PDBEntry("3A6S", null, null, null);
+ pdb2 = new PDBEntry("3A6S", null, null, null);
+ pdb2.setProperty("hello", "moon");
+ assertTrue(pdb1.updateFrom(pdb2));
+ assertEquals(pdb1.getProperty("hello"), "moon");
+
+ /*
+ * different id but authoritative
+ */
+ pdb1 = new PDBEntry("af:1xyz", "A", null, "a/b/c/File");
+ pdb2 = new PDBEntry("af-1xyz", "A", null, "a/b/c/File");
+ pdb1.setAuthoritative(true);
+
+ assertTrue(pdb1.isAuthoritative());
+ assertFalse(pdb2.isAuthoritative());
+ // can update pdb1 (authoritative) from pdb2 (non-authoritative)
+ assertTrue(pdb1.updateFrom(pdb2));
+ // but the ID must remain the same
+ assertEquals(pdb1.getId(), "af:1xyz");
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testConstructor_fromDbref()
+ {
+ PDBEntry pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70"));
+ assertEquals(pdb.getId(), "1A70");
+ assertNull(pdb.getChainCode());
+ assertNull(pdb.getType());
+ assertNull(pdb.getFile());
+
+ /*
+ * from dbref with chain code appended
+ */
+ pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70B"));
+ assertEquals(pdb.getId(), "1A70");
+ assertEquals(pdb.getChainCode(), "B");
+
+ /*
+ * from dbref with overlong accession
+ */
+ pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70BC"));
+ assertEquals(pdb.getId(), "1A70BC");
+ assertNull(pdb.getChainCode());
+
+ /*
+ * from dbref which is not for PDB
+ */